Sequencing the genome of antibiotic-resistant bacteria

A REPORT this week from Madrid recounts the novel use of the latest genomic sequencing system to unravel some of the secrets of new strains of the bacterium of Klebsiella pneunomiae.

Researchers at the University Hospital La Paz Research Institute in Madrid, known as IdiPAZ, used a Roche 454 GS FLX+ genomic sequencing system to study three strains of the microbe, isolated from a serious outbreak recently at a hospital in the city. These are understood to be some of the first sequencings of this particular species, and the scientists hope their work will provide new insight into the development of antibiotic resistance.

Klebsiella pneumoniae is common in the mouth and gut of healthy humans, and rarely causes disease. However this microorganism has a substantial capacity for opportunistic mutation, including the ability to acquire resistance to antibiotics.

Three strains of pathogenic K pneumoniae with varying levels of antibiotic resistance were isolated in the microbiology department at IdiPAZ, and sequenced at the laboratories of LifeSequencing in Valencia. There the long-read GS FLX+ system, developed by 454 Life Sciences, proved its usefulness.

Sequencing data obtained by the GS FLX+ was assembled using GS De Novo Assembler software, and functional annotation used to identify the relevant genes codified in the three genomes. The rich functional annotation was provided by BG7, a system developed by Era 7 Bioinformatics.

The three strains showed increasing resistance to a wide range of the most commonly used antibiotics at the hospital. By considering the variations in their genomes, both between the strains and compared to the genomes of other bacteria, the researchers hope to discover how the resistance mechanism is developed and, ultimately, find ways to overcome it.

Leave a Reply

Your email address will not be published. Required fields are marked *